Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests

Evolutionary Applications

Volumn 5, Issue 7, 2012, Pages 762-775

  Mosca, Elena ^a,b   Eckert, Andrew J ^c   Liechty, John D ^a   Wegrzyn, Jill L ^a   La Porta, Nicola ^b   Vendramin, Giovanni G ^d   Neale, David B ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b RESEARCH AND INNOVATION CENTRE   (Italy)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^d CNR   (Italy)

Author keywords

Candidate gene; Neutrality tests; Nucleotide diversity; Single nucleotide polymorphisms

Indexed keywords

EID: 84868197818     PISSN: 17524563     EISSN: 17524571     Source Type: Journal    
DOI: 10.1111/j.1752-4571.2012.00256.x     Document Type: Article

References (89)

1. Aitken, S. N., and M. Hannerz 2001. Genecology and gene resource management strategies for conifer cold hardiness. In F.J. Bigras and S. J. Columbo, eds. Conifer Cold Hardiness. pp. 23-53. Kluwer Academic Publishers, Dordrecht, The Netherlands.
2. Aitken, S. N., S. Yeaman, J. A. Holliday, T. Wang, and S. Curtis-McLane 2008. Adaptation, migration or extirpation: climate change outcomes for tree populations. Evolutionary Applications1(1):95-111.
3. Ascencio-Ibáñez, J.-T., R. Sozzani, T.-L. Lee, T.-M. Chu, R.-D. Wolfinger, R. Cella, and L. Hanley-Bowdoin 2008. Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during Geminivirus Infection. Plant Physiology148:436-454.
4. Belokon, M. M., Y. S. Belokon, D. V. Politov, and Y. P. Altukhov 2005. Allozyme polymorphism of Swiss stone pine Pinus cembra L. in mountain populations of the Alps and the Eastern Carpathians. Russian Journal of Genetics41(11):1268-1280.
5. Bentsinka, L., and M. Koornneef 2008. Seed dormancy and germination. The Arabidopsis Book, Number 6.
6. Bonan, G. B. 2008. Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science320(5882):1444-1449.
7. Camarero, J. J., E. Gutierrez, M. J. Fortin, and E. Ribbens 2005. Spatial patterns of tree recruitment in a relict population of Pinus uncinata: forest expansion through stratified diffusion. Journal of Biogeography32(11):1979-1992.
8. Cannone, N., G. Diolaiuti, M. Guglielmin, and C. Smiraglia 2008. Accelerating climate change impacts on Alpine glacier forefields ecosystems in the European Alps. Ecological Applications18(3):637-648.
9. Christensen, K. L. 1987. Taxonomic revision of the Pinus mugo complex and P. rhaetica (P. mugo sylvestris) (Pinaceae). Nordic Journal of Botany7(4):383-408.
10. Crimmins, S. M., S. Z. Dobrowski, J. A. Greenberg, J. T. Abatzoglou, and A. R. Mynsberge 2011. Changes in climatic water balance drive downhill shift in plant species' optimum elevations. Science331:324-327.
11. Dal Bosco, C., L. Lezhneva, A. Biehl, D. Leister, H. Strotmann, G. Wanner, and J. Meurer 2004. Inactivation of the chloroplast ATP synthase y subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. The Journal of Biological Chemistry279(2):1060-1069.
12. Devlin, B., K. Roeder, and L. Wasserman 2000. Genomic control for association studies: a semiparametric test to detect excess-haplotype sharing. Biostatistics1(4):369-387.
13. Dreher, K., and J. Callis 2007. Ubiquitin, hormones and biotic stress in plants. Annals of Botany99:787-822.
14. Eckert, A. J., and B. D. Hall 2006. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution40(1):166-182.
15. Eckert, A. J., J. L. Wegrzyn, B. Pande, K. D. Jermstad, J. M. Lee, J. D. Liechty, B. R. Tearse et al.2009. Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii). Genetics183(1):289-298.
16. Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. Dana Nelson, J. Ross-Ibarra, and S. C. González-Martínez 2010a. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics185(3):969-982.
17. Eckert, A. J., J. D. Liechty, B. R. Tearse, B. Pande, and D. B. Neale 2010b. DnaSAM: software to perform neutrality testing for large datasets with complex null models. Molecular Ecology Resources10(3):542-545.
18. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high Throughput. Nucleic Acids Research32(5):1792-1797.
19. Eveno, E., C. Collada, M. A. Guevara, V. Léger, A. Soto, L. Díaz, P. Léger, 2008. Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses. Molecular Biology and Evolution25(2):417-437.
20. Ewens, W. J. 1972. The sampling theory of selectively neutral alleles. Theoretical Population Biology3:87-112.
21. Farjon, A. 1990. Pinaceae: drawings and descriptions of the genera Abies, Cedrus, Pseudolarix, Keteleeria, Nothotsuga, Tsuga, Cathaya, Pseudotsuga, Larix and Picea. Regnum Veg. 121. (Pinaceae).
22. Fay, J. C., and C. I.. Wu 2000. Hitchhiking under positive Darwinian selection. Genetics155(3):1405-1413.
23. Gamache, I., and S. Payette 2004. Height growth response of tree line black spruce to recent climate warming across the forest-tundra of eastern Canada. Journal of Ecology35(5):1-845.
24. Garnier-Géré, P. H., and P. K. Ades 2001. Environmental surrogates for predicting and conserving adaptive genetic variability in tree species. Conservation Biology15:1632-1644.
25. Garvin, M. R., K. Saitoh, and A. J. Gharrett 2010. Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources10:915-934.
26. Gernandt, D. S., S. Magallón, G. G. López, O. Z. Flores, A. Willyard, and A. Listonk 2008. Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. International Journal of Plant Sciences169(8):1086-1099.
27. González-Martínez, S. C., E. Ersoz, G. R. Brown, N. C. Wheeler, and D. B. Neale 2006. DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics172(3):1915-1926.
28. González-Martínez, S. C., D. Huber, E. Ersoz, J. M. Davis, and D. B. Neale 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity101:19-26.
29. Gordon, D., C. Abajian, and P. Green 1998. Consed: a graphical tool for sequence finishing. Genome research8(3):195-202.
30. Grace, J. 2002. Impacts of climate change on the tree line. Annals of Botany90(4):537-544.
31. Grivet, D., F. Sebastiani, S. G. González-Martínez, and G. G. Vendramin 2009. Patterns of polymorphism resulting from long-range colonization in the Mediterranean conifer Aleppo pine. New Phytologist184(4):1016-1028.
32. Grivet, D., F. Sebastiani, R. Alía, T. Bataillon, S. Torre, M. Zabal-Aguirre, G. G. Vendramin et al.2011. Molecular footprints of local adaptation in two Mediterranean conifers. Molecular Biology and Evolution28(1):101-116.
33. Gugerli, F., M. Rüegg, and G. G. Vendramin 2009. Gradual decline in genetic diversity in Swiss stone pine populations (Pinus cembra) across Switzerland suggests postglacial re-colonization into the Alps from a common eastern glacial refugium. Botanica Helvetica119:13-22.
34. Halkier, B. A., and J. Gershenzon 2006. Biology and biochemistry of glucosinolates. Annual Review of Plant Biology57:303-333.
35. Heuertz, M., J. Teufel, S. C. González-Martínez, A. Soto, B. Fady, R. Alía, and G. G. Vendramin 2010. Geography determines genetic relationships between species of mountain pine (Pinus mugo complex) in Western Europe. Journal of Biogeography37(3):541-556.
36. Höhn, M., A. Brán, and G. G. Vendramin 2005. Genetic analysis of Swiss stone pine populations (Pinus cembra L. subsp. cembra) from the Carpathians using chloroplast microsatellites. Acta Silvatica et Lignaria Hungarica1:39-47.
37. Höhn, M., F. Gugerli, P. Abran et al.2009. Variation in the chloroplast DNA of Swiss stone pine (Pinus cembra L.) reflects contrasting post-glacial history of populations from the Carpathians and the Alps. Journal of Biogeography36(9):1798-1806.
38. Holliday, J. A., M. Ritland, and S. N. Aitken 2010. Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests. Molecular Ecology19:3857-3864.
39. Hudson, R. R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics Applications Note18(2):337-338.
40. Kelley, J. L., J. Madeoy, J. C. Calhoun, W. Swanson, and J. M Akey 2006. Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research16(8):980-989.
41. Kelly, J. K. 1997. A test of neutrality based on interlocus associations. Genetics146(3):1197-1206.
42. Konishi, T., K. Shinohara, K. Yamada, and Y. Sasaki 1996. Acetyl- CoA carboxylase in higher plants: most plants other than gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiology37:117-122.
43. Li-Beisson, Y., B. Shorrosh, F. Beisson et al.2010. Acyl-lipid metabolism. The Arabidopsis Book 8
44. Liepelt, S., R. Cheddadi, J. De-Beaulieu et al.2009. Postglacial range expansion and its genetic imprints in Abies alba (Mill.) - a synthesis from palaeobotanic and genetic data. Review of Palaeobotany and Palynology 153(1-2)13:9-149.
45. Lozano-Durán, R., T. Rosas-Díaz, G. Gusmaroli, A. P. Luna, L. Taconnat, W. X. Deng, and E. R. Bejaranoa 2011. Geminiviruses subvert ubiquitination by altering CSN-mediated derubylation of SCF E3 ligase complexes and inhibit jasmonate signaling in Arabidopsis thaliana. The Plant Cell23:1014-1032.
46. Luikart, G., P. R. England, D. Tallmon, S. Jordan, and P. Taberlet 2003. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics4:981-994.
47. Ma, X.-F., A. E. Szmidt, and X.-R. Wang 2006. Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci. Molecular Biology and Evolution23(4):807-816.
48. Meshinev, T., I. Apostolova, and E. Koleva 2000. Influence of warming on timberline rising: a case study on Pinus peuce Griseb. in Bulgaria. Phytocoenologia30:431-438.
49. Mikkelsen, M. D., P. Naur, and B. A. Halkier 2004. Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis. The Plant Journal37:770-777.
50. Monteleone, I., D. Ferrazzini, and P. Belletti 2006. Effectiveness of neutral RAPD markers to detect genetic divergence between the subspecies uncinata and mugo of Pinus mugo Turra. Silva Fennica40(3):391-406.
51. Namroud, M.C., J. Beaulieu, N. Juge, J. Laroche, and J. Bousquet 2008. Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Molecular Ecology17:3599-3613.
52. Neale, D. B., and O. Savolainen 2004. Association genetics of complex traits in conifers. Trends in Plant Science9(7):325-330.
53. Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, NY.
54. Palmé, A. E., M. Wright, and O. Savolainen 2008. Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps. Molecular Biology and Evolution25(12):2567-2577.
55. Palmé, A. E., T. Pyhäjärvi, W. Wachowiak, and O. Savolainen 2009. Selection on nuclear genes in a Pinus phylogeny. Molecular Biology and Evolution26(4):893-905.
56. Parchman, T. L., K. S. Geist, J. A. Grahnen, C. W. Benkman, and C. A. Buerkle 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation and marker discovery. BMC Genomics11:180-196.
57. Pautasso, M. 2009. Geographical genetics and the conservation of forest trees. Perspectives in Plant Ecology, Evolution and Systematic11:157-189.
58. Peñuelas, J., and M. Boada 2003. A global change-induced biome shift in the Montseny mountains (NE Spain). Global Change Biology9(2):131-140.
59. Pyhäjärvi, T., M. R. García-Gil, T. Knürr, M. Mikkonen, W. Wachowiak, and O. Savolainen 2007. Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics177(3):1713-1724.
60. R Development Core Team. 2007. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org (accessed on 10 March 2011).
61. Rambaut, A. 19962002. Sequence alignment editor v2.0a11. http://tree.bio.ed.ac.uk/software/seal/ (accessed on 14 March 2011).
62. Rogers, D. L., C. I. Millar, and R. D. Westfall 1999. Fine-scale genetic structure of whitebark pine (Pinus albicaulis): associations with watershed and growth form. Evolution53:74-90.
63. Rubner, K. 1953. Die Pflanzengeographischen Grundlagen des Waldbaues. Neumann, Radebeul, Berlin.
64. Sandoz, H. 1983. Sur la plausibilité de l'installation de refuges pléistocènes du Pin mugho ou Pin pumilo (Pinus mughus Scopoli = Pinus pumilio Haenke) dans la basse vallée de la Durance (Provence occidentale - France). Revue Générale de Botanique90:23-41.
65. Santner, A., and M. Estelle 2009. Recent advances and emerging trends in plant hormone signalling. Nature459:1071-1078.
66. Savolainen, O., and T. Pyhäjärvi 2007. Genomic diversity in forest trees. Current Opinion Plant Biology10:1-6.
67. Schaberg, P. G., D. H. DeHayes, G. J. Hawley, and S. E. Nijensohn 2008. Anthropogenic alterations of genetic diversity within tree populations: implications for forest ecosystem resilience. Forest Ecology and Management256(5):855-862.
68. Scotti-Saintagne, C., S. Mariette, I. Porth, P. G. Goicoechea, T. Barreneche, C. Bodenes, K. Burg et al.2004. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics168:1615-1626.
69. Shiraishi, S., and S. Shiraishi 2011. Nucleotide diversities and genetic relationship in the three Japanese pine species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis. Diversity3(1):121-135.
70. Städler, T., B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber 2009. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics182(1):205-216.
71. Sun, T.-P. 2010. Gibberellin-GID1-DELLA: a pivotal regulatory module for plant growth and development. Plant Physiology154:2567-2570.
72. Synek, L., N. Schlager, M. Eliáš, M. Quentin, M.-T. Hauser, and V. Žárský 2006. AtEXO70A1, a member of a family of putative exocyst subunits specifically expanded in land plants, is important for polar growth and plant development. Plant Journal48(1):54-72.
73. Syring, J., R. F. del Castillo, R. Cronn, and A. Liston 2007. Multiple nuclear loci reveal the distinctiveness of the threatened, neotropical Pinus Chiapensis. Systematic Botany32(4):703-717.
74. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics105:437-460.
75. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics123:585-595.
76. Taylor, N. L., Y. F. Tan, R. P. Jacoby, and A. H. Millar 2009. Abiotic environmental stress induced changes in the Arabidopsis thaliana chloroplast, mitochondria and peroxisome proteomes. Journal of proteomics72(3):367-378.
77. Theurillat, J., and A. Guisan 2001. Potential impact of climate change on vegetation in the European alps: a review. Climatic Change50:77-109.
78. Thornton, K. 2003. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics19(17):2325-2327.
79. Tomback, D. F. 2005. The impact of seed dispersal by Clark's nutcracker on whitebark Pine: multi-scale perspective on a high mountain mutualism. In G. Broll, and B. Keplin, eds. Mountain Ecosystems: Studies in Treeline Ecology. pp. 181-201. Springer, Berlin, Germany.
80. Wachowiak, W., and W. Prus-Glłowacki 2008. Hybridisation processes in sympatric populations of pines Pinus sylvestris L., P. mugo Turra and P. uliginosa Neumann. Plant Systematics and Evolution271:29-40.
81. Wachowiak, W., P. A. Balk, and O. Savolainen 2009. Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.). Tree Genetics & Genomes5(1):117-132.
82. Wang, Y., C. Ribot, E. Rezzonico, and P. Yves 2004. Structure and expression profile of the Arabidopsis PHO1 gene family indicates a broad role in inorganic phosphate homeostasis. Plant Physiology135:400-411.
83. Wang, Z., M. Gerstein, and M. Snyder 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics10:57-63.
84. Watterson, G. A.. 1975. On the number of segregating sites. Theoretical Population Biology7:256-276.
85. Wegrzyn, J. L., J. M. Lee, J. Liechty, and D. B. Neale 2009. PineSAP - pine alignment and SNP identification pipeline. Bioinformatics25(19):2609-2610.
86. Willyard, A., J. Syring, D. S. Gernandt, A. Liston, and Cronn. R 2007. Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution24:90-101.
87. Yang, T., L. Bar-Peled, L. Gebhart, S. G. Lee, and M. Bar-Peled 2009. Identification of galacturonic acid-1-phosphate kinase, a new member of the GHMP kinase superfamily in plants, and comparison with galactose-1-phosphate kinase. The Journal of Biological Chemistry284(32):21526-21535.
88. Zeng, K., Y.-X. Fu, S. Shi, and C.-I. Wu 2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics174(3):1431-1439.
89. Zeng, K., S. Suhua, and C.-I. Wu 2007. Compound tests for the detection of hitchhiking under positive selection. Molecular Biology & Evolution24:1898-1908.